Kinetic Modeling of the Genetic Information Processes in a Minimal Cell

Abstract

JCVI-syn3A is a minimal bacterial cell with a 543 kbp genome consisting of 493 genes. For this slow growing minimal cell with a 105 min doubling time, we recently established the essential metabolism including the transport of required nutrients from the environment, the gene map, and genome-wide proteomics. Of the 452 protein-coding genes, 143 are assigned to metabolism and 212 are assigned to genetic information processing. Using genome-wide proteomics and experimentally measured kinetic parameters from the literature we present here kinetic models for the genetic information processes of DNA replication, replication initiation, transcription, and translation which are solved stochastically and averaged over 1,000 replicates/cells. The model predicts the time required for replication initiation and DNA replication to be 8 and 50 min on average respectively and the number of proteins and ribosomal components to be approximately doubled in a cell cycle. The model of genetic information processing when combined with the essential metabolic and cell growth networks will provide a powerful platform for studying the fundamental principles of life.

Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps

“…The configurations resulting from the SAP model of the bacterial chromosome are directly transferrable to the 8 nm lattice representation used for LM simulations of whole Syn3A cells through a coarse-graining procedure. The coarse-grained chromosome configurations specify the spatial heterogeneities caused by DNA-crowding in whole-cell kinetic models of Syn3A and define the spatial locations of genes to investigate spatial and temporal correlations in gene expression (Weng and Xiao, 2014;Thornburg et al, 2019). Future work will focus on assigning chromosomal interactions based on improved experimental 3C-Seq libraries, improving the model to include dynamic formation and relaxation of supercoiling and plectonemic loops, and incorporating dynamic representations of the chromosome (Miermans and Broedersz, 2020) within the LM simulations, which will include DNA diffusion and chromosome replication.…”

“…Figure 8 shows the coarsegraining of a chromosome configuration in the small cell. The kinetic model of genetic information processing in Syn3A (Thornburg et al, 2019) can then be extended to include the effects of RNA polymerases diffusing between the spatial locations of genes within the chromosome (Weng and Xiao, 2014).…”

“…JCVI-syn3A is a genetically minimal bacterial cell, consisting of 493 genes and a single short 543 kbp circular chromosome derived from a Gram-positive bacterium, Mycoplasma mycoides. Previous work established genome-scale gene essentiality and proteomics data along with its essential metabolic network (Hutchison et al, 2016;Breuer et al, 2019) and a kinetic model of genetic information processing (Thornburg et al, 2019). The kinetic model of genetic information processes of DNA replication, transcription, and translation requires positions and length of genes along the chromosome.…”

Fundamental behaviors emerge from simulations of a living minimal cell

“…N Enzyme:Template (Equation 6) Rather than depending on the time-dependent template counts, the rates are now dependent on the count of the enzyme-template bound state N Enzyme:Template , for example N RNAP:gene;i once the enzyme and/or template has diffused to the other and bind. All sequences were read from the Syn3A NCBI entry (CP016816.2) using Biopython (Cock et al, 2009) DNA replication initiation Thornburg et al (2019) identified the three neighboring 9 bp affinity sites where domain DnaA(IV) is known to bind to dsDNA based on the crystallographic study (PDB: 1j1v and PDB: 3r8f) from Erzberger et al (2006); Duderstadt et al (2011). We simulate reactions for DnaA(IV) binding to the 9 bp high affinity site next to the origin, TTATCCACA, and subsequent binding to two neighboring low affinity sites (7/9 bp matches 2 and 1 bp away).…”

A Multi-Scale Approach to Modeling E. coli Chemotaxis

“…For transcription and translation, the algorithm uses a polymerization function to move the polymerases across the DNA or mRNA template at a set elongation rate and pull the required base pairs (nucleotides or amino acids) out of the available metabolite pools; mass is conserved as these base pairs are converted into polymers. Energy requirements for expression are based on ATP hydrolysis for each synthesized or degraded base pair [ 49 ]; the ATP is pulled out of a metabolite pool and converted into ADP.…”